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PspF DNA-binding transcriptional dual regulator

Synonyms: PspF, PspF
The transcription factor PspF, for "Phage shock protein F," is a bacterial enhancer-binding protein required for σ54-dependent transcription activation [6, 7]. This regulator activates the transcription of the psp regulon, and it is negatively autoregulated and coordinately activated by transcription of the divergent operon psp [4, 5, 7]. The integration host factor facilitates control of the psp regulon [2, 5, 8]. The psp regulon is defined like the phage shock protein system, which is involved in protecting the bacterium during infectious processes [5, 7]. The synthesis of this regulon is induced when Escherichia coli is grown under different extracytoplasmic stress conditions and upon infection by filamentous phage (phage shock) [9, 10, 11, 12, 13, 14].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PspF Functional   nd nd
PspF Functional   nd nd
Evolutionary Family: EBP
TFBs length: 17
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: pspF
  Genome position: 1366935-1367912
  Length: 978 bp / 325 aa
Operon name: pspF
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) pspA, pspB, pspC, pspD, pspE, pspF, pspG, pspH
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
prophage genes and phage related functions (5)
operon (4)
inhibition / activation of enzymes (1)
Transcription related (1)
activator (1)
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Regulated operon(s) pspABCDE, pspF, pspGH
First gene in the operon(s) pspA, pspF, pspG
Simple and complex regulons IHF,PspF
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor regulation    

Transcription factor binding sites (TFBSs) arrangements

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  PspF activator pspAp Sigma54 -119.0 -160.0 pspA, pspB, pspC, pspD, pspE
1367911 1367927 [GEA], [BCE], [BPP] [1], [2], [3]
  PspF activator pspAp Sigma54 -99.0 -140.0 pspA, pspB, pspC, pspD, pspE
1367931 1367947 [GEA], [BCE], [BPP] [1], [2], [3]
  PspF repressor pspFp1 Sigma70 7.0 -27.0 pspF
1367931 1367947 [GEA], [BCE], [BPP] [1], [4]
  PspF repressor pspFp1 Sigma70 27.0 -7.0 pspF
1367911 1367927 [GEA], [BCE], [BPP] [1], [4]
  PspF activator pspGp Sigma54 -87.0 -111.0 pspG, pspH
4262721 4262737 [GEA], [BPP], [ICA] [5]

Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


 [1] Engl C., Jovanovic G., Brackston RD., Kotta-Loizou I., Buck M., 2020, The route to transcription initiation determines the mode of transcriptional bursting in E. coli., Nat Commun 11(1):2422

 [2] Jovanovic G., Model P., 1997, PspF and IHF bind co-operatively in the psp promoter-regulatory region of Escherichia coli., Mol Microbiol 25(3):473-81

 [3] Jovanovic G., Rakonjac J., Model P., 1999, In vivo and in vitro activities of the Escherichia coli sigma54 transcription activator, PspF, and its DNA-binding mutant, PspFDeltaHTH., J Mol Biol 285(2):469-83

 [4] Jovanovic G., Dworkin J., Model P., 1997, Autogenous control of PspF, a constitutively active enhancer-binding protein of Escherichia coli., J Bacteriol 179(16):5232-7

 [5] Lloyd LJ., Jones SE., Jovanovic G., Gyaneshwar P., Rolfe MD., Thompson A., Hinton JC., Buck M., 2004, Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein G (PspG)., J Biol Chem 279(53):55707-14

 [6] Rappas M, Bose D, Zhang X, 2007, Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription., Curr Opin Struct Biol, 17(1):110 10.1016/

 [7] Jovanovic G., Weiner L., Model P., 1996, Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon., J Bacteriol 178(7):1936-45

 [8] Dworkin J, Jovanovic G, Model P, 1997, Role of upstream activation sequences and integration host factor in transcriptional activation by the constitutively active prokaryotic enhancer-binding protein PspF., J Mol Biol, 273(2):377 10.1006/jmbi.1997.1317

 [9] Weiner L., Brissette JL., Model P., 1991, Stress-induced expression of the Escherichia coli phage shock protein operon is dependent on sigma 54 and modulated by positive and negative feedback mechanisms., Genes Dev 5(10):1912-23

 [10] Jovanovic G, Lloyd LJ, Stumpf MPH, Mayhew AJ, Buck M, 2006, Induction and function of the phage shock protein extracytoplasmic stress response in Escherichia coli., J Biol Chem, 281(30):21147 10.1074/jbc.M602323200

 [11] Model P, Jovanovic G, Dworkin J, 1997, The Escherichia coli phage-shock-protein (psp) operon., Mol Microbiol, 24(2):255 10.1046/j.1365-2958.1997.3481712.x

 [12] Darwin AJ, 2005, The phage-shock-protein response., Mol Microbiol, 57(3):621 10.1111/j.1365-2958.2005.04694.x

 [13] Brissette JL., Weiner L., Ripmaster TL., Model P., 1991, Characterization and sequence of the Escherichia coli stress-induced psp operon., J Mol Biol 220(1):35-48

 [14] Kobayashi H, Yamamoto M, Aono R, 1998, Appearance of a stress-response protein, phage-shock protein A, in Escherichia coli exposed to hydrophobic organic solvents., Microbiology (Reading), 144 ( Pt 2)(None):353 10.1099/00221287-144-2-353

 [15] Elderkin S., Jones S., Schumacher J., Studholme D., Buck M., 2002, Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF., J Mol Biol 320(1):23-37

 [16] Heidrich ES, Brüser T, 2018, Evidence for a second regulatory binding site on PspF that is occupied by the C-terminal domain of PspA., PLoS One, 13(6):e0198564 10.1371/journal.pone.0198564

 [17] Dworkin J, Jovanovic G, Model P, 2000, The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription., J Bacteriol, 182(2):311 10.1128/JB.182.2.311-319.2000

 [18] Zhang N, Simpson T, Lawton E, Uzdavinys P, Joly N, Burrows P, Buck M, 2013, A key hydrophobic patch identified in an AAA? protein essential for its in trans inhibitory regulation., J Mol Biol, 425(15):2656 10.1016/j.jmb.2013.04.024

 [19] Mehta P, Jovanovic G, Lenn T, Bruckbauer A, Engl C, Ying L, Buck M, 2013, Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells., Nat Commun, 4(None):1997 10.1038/ncomms2997

 [20] Weiner L., Brissette JL., Ramani N., Model P., 1995, Analysis of the proteins and cis-acting elements regulating the stress-induced phage shock protein operon., Nucleic Acids Res 23(11):2030-6

 [21] Adams H, Teertstra W, Demmers J, Boesten R, Tommassen J, 2003, Interactions between phage-shock proteins in Escherichia coli., J Bacteriol, 185(4):1174 10.1128/JB.185.4.1174-1180.2003

 [22] Chaney M, Grande R, Wigneshweraraj SR, Cannon W, Casaz P, Gallegos MT, Schumacher J, Jones S, Elderkin S, Dago AE, Morett E, Buck M, 2001, Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action., Genes Dev, 15(17):2282 10.1101/gad.205501

 [23] Cannon WV, Schumacher J, Buck M, 2004, Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein., Nucleic Acids Res, 32(15):4596 10.1093/nar/gkh755

 [24] Lew CM, Gralla JD, 2002, New roles for conserved regions within a sigma 54-dependent enhancer-binding protein., J Biol Chem, 277(44):41517 10.1074/jbc.M206912200

 [25] Bordes P, Wigneshweraraj SR, Schumacher J, Zhang X, Chaney M, Buck M, 2003, The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: identifying a surface that binds sigma 54., Proc Natl Acad Sci U S A, 100(5):2278 10.1073/pnas.0537525100

 [26] Cannon W, Bordes P, Wigneshweraraj SR, Buck M, 2003, Nucleotide-dependent triggering of RNA polymerase-DNA interactions by an AAA regulator of transcription., J Biol Chem, 278(22):19815 10.1074/jbc.M301296200

 [27] Jovanovic G, Model P, 1997, The RIB element in the goaG-pspF intergenic region of Escherichia coli., J Bacteriol, 179(10):3095 10.1128/jb.179.10.3095-3102.1997

 [28] Elderkin S, Bordes P, Jones S, Rappas M, Buck M, 2005, Molecular determinants for PspA-mediated repression of the AAA transcriptional activator PspF., J Bacteriol, 187(9):3238 10.1128/JB.187.9.3238-3248.2005

 [29] Darbari VC, Lawton E, Lu D, Burrows PC, Wiesler S, Joly N, Zhang N, Zhang X, Buck M, 2014, Molecular basis of nucleotide-dependent substrate engagement and remodeling by an AAA+ activator., Nucleic Acids Res, 42(14):9249 10.1093/nar/gku588

 [30] Schumacher J, Zhang X, Jones S, Bordes P, Buck M, 2004, ATP-dependent transcriptional activation by bacterial PspF AAA+protein., J Mol Biol, 338(5):863 10.1016/j.jmb.2004.02.071

 [31] Joly N, Schumacher J, Buck M, 2006, Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator., J Biol Chem, 281(46):34997 10.1074/jbc.M606628200

 [32] Bordes P, Wigneshweraraj SR, Zhang X, Buck M, 2004, Sigma54-dependent transcription activator phage shock protein F of Escherichia coli: a fragmentation approach to identify sequences that contribute to self-association., Biochem J, 378(Pt 3):735 10.1042/BJ20031464

 [33] Ogura T, Wilkinson AJ, 2001, AAA+ superfamily ATPases: common structure--diverse function., Genes Cells, 6(7):575 10.1046/j.1365-2443.2001.00447.x

 [34] Walker JE, Saraste M, Runswick MJ, Gay NJ, 1982, Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold., EMBO J, 1(8):945 None

 [35] Bose D, Joly N, Pape T, Rappas M, Schumacher J, Buck M, Zhang X, 2008, Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins., Biochem Soc Trans, 36(Pt 1):83 10.1042/BST0360083

 [36] Zhang N, Joly N, Buck M, 2012, A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements., Nucleic Acids Res, 40(18):9139 10.1093/nar/gks661

 [37] Dago AE, Wigneshweraraj SR, Buck M, Morett E, 2007, A role for the conserved GAFTGA motif of AAA+ transcription activators in sensing promoter DNA conformation., J Biol Chem, 282(2):1087 10.1074/jbc.M608715200

 [38] Bordes P, Wigneshweraraj SR, Chaney M, Dago AE, Morett E, Buck M, 2004, Communication between Esigma(54) , promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF sigma-dependent activator during transcription activation., Mol Microbiol, 54(2):489 10.1111/j.1365-2958.2004.04280.x

 [39] Zhang N, Joly N, Burrows PC, Jovanovic M, Wigneshweraraj SR, Buck M, 2009, The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins., Nucleic Acids Res, 37(18):5981 10.1093/nar/gkp658

 [40] Burrows PC, Schumacher J, Amartey S, Ghosh T, Burgis TA, Zhang X, Nixon BT, Buck M, 2009, Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein., Mol Microbiol, 73(4):519 10.1111/j.1365-2958.2009.06744.x

 [41] Schumacher J, Joly N, Rappas M, Bradley D, Wigneshweraraj SR, Zhang X, Buck M, 2007, Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase., J Biol Chem, 282(13):9825 10.1074/jbc.M611532200

 [42] Joly N, Buck M, 2011, Single chain forms of the enhancer binding protein PspF provide insights into geometric requirements for gene activation., J Biol Chem, 286(14):12734 10.1074/jbc.M110.203554

 [43] Tucker PA, Sallai L, 2007, The AAA+ superfamily--a myriad of motions., Curr Opin Struct Biol, 17(6):641 10.1016/

 [44] Schumacher J, Joly N, Rappas M, Zhang X, Buck M, 2006, Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation., J Struct Biol, 156(1):190 10.1016/j.jsb.2006.01.006